Next-generation Sequencing (NGS) technologies have made whole-genome sequencing (WGS) routine, and various target enrichment methods have enabled researchers to focus sequencing power on the most important regions of interest. However, there is still a need for better methods of applying NGS to difficult target DNAs, such as formalin-fixed, paraffin-embedded (FFPE) solid tumor samples, cell-free or circulating tumor DNA (cfDNA/ctDNA), or damaged DNA samples. Problems associated with sequencing such targets include that the amounts of DNA can be very small, the DNA can be very short (e.g., fragmented DNA) or chemically modified, and the allele frequencies can be very low. These problems necessitate the capture of many DNA templates.
In particular, it is challenging to sequence smaller fragments of genomic DNA using transposase-based tagging methods because many of those methods require the insertion of two adjacent transposases to produce a fragment having the appropriate sequencing primer binding site on each end, and such small fragments are often not long enough to accommodate adjacent transposases. The present disclosure provides inter alia compositions and methods to improve tagging and amplifying such DNA samples for downstream analysis, e.g., next generation sequencing.